Roll 'lumped' genera to lowest common taxonomic resolution

This function replaces all 'lump' genera (generated by getInvertData(taxonFix = "lump")) with the lowest common taxonomic resolution for all genera in the lumped genus. Designed to be implemented with getInvertData(taxonLevel = "Mixed").

Usage

lumpRollUp(inputdataset)

Arguments

inputdataset

Input dataset that must be generated from getInvertData().

Value

A taxa by sample data frame with site, stream reach, and sample information.

Details

In some instances, like when calculating MMIs for example, it may be useful to roll the 11 "lumped" genera to their lowest common taxonomic resolution (Subfamily, Family, or Order). This function does not adjust "slash" taxa, or those organisms that were identified to a slash genus designation in the lab (see the Getting Started vignette for more details). This function gathers the lowest common taxonomic resolution all lump genus members share. The function then replaces the "lump genus" name (e.g., Elimia/Pleurocera) with the lowest common taxonomic resolution designation (e.g., Pleuroceridae). The function then sums occurrence or density data within duplicate broader taxonomic designations. For instance, if taxonLevel = "Mixed", then observations among duplicated taxonomic unit columns would be summed (occurrences summed then converted to 0/1).

The input dataset should be directly generated by getInvertData(), with taxonFix = "lump".

Author

Michael Mahon

Examples

if (FALSE) {
Inverts <- getInvertData(taxonLevel = "Mixed",
                         taxonFix = "lump")

##roll lumped genera to lowest common taxonomic unit
InvertsUpdatedLump <- lumpRollUp(Inverts)

}